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For: Masuda T, Saito N, Tomita M, Ishihama Y. Unbiased quantitation of Escherichia coli membrane proteome using phase transfer surfactants. Mol Cell Proteomics 2009;8:2770-7. [PMID: 19767571 DOI: 10.1074/mcp.m900240-mcp200] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
Number Cited by Other Article(s)
1
Ouchi K, Masuda T, Yonemaru K, Isono K, Ohya Y, Shiraki N, Tasaki M, Inomata Y, Ueda M, Era T, Kume S, Ando Y, Jono H. Dynamic changes of intracellular signals in ATTR Tyr114Cys amyloidosis. Biochem Biophys Rep 2025;42:102012. [PMID: 40275963 PMCID: PMC12020847 DOI: 10.1016/j.bbrep.2025.102012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2024] [Revised: 04/04/2025] [Accepted: 04/07/2025] [Indexed: 04/26/2025]  Open
2
Nemoto S, Uchida K, Kubota T, Nakayama M, Han YW, Koyasu S, Ohno H. Tetraspanin7 in adipose tissue remodeling and its impact on metabolic health. Mol Metab 2025;97:102168. [PMID: 40368161 DOI: 10.1016/j.molmet.2025.102168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2025] [Revised: 05/07/2025] [Accepted: 05/08/2025] [Indexed: 05/16/2025]  Open
3
Hasumi M, Ito H, Machida K, Niwa T, Taminato T, Nagai Y, Imataka H, Taguchi H. Dissecting the mechanism of NOP56 GGCCUG repeat-associated non-AUG translation using cell-free translation systems. J Biol Chem 2025;301:108360. [PMID: 40015643 PMCID: PMC11979933 DOI: 10.1016/j.jbc.2025.108360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2024] [Revised: 02/18/2025] [Accepted: 02/20/2025] [Indexed: 03/01/2025]  Open
4
Morishima T, Fakruddin M, Kanamori Y, Masuda T, Ogawa A, Wang Y, Schoonenberg VAC, Butter F, Arima Y, Akaike T, Moroishi T, Tomizawa K, Suda T, Wei FY, Takizawa H. Mitochondrial translation regulates terminal erythroid differentiation by maintaining iron homeostasis. SCIENCE ADVANCES 2025;11:eadu3011. [PMID: 39983002 PMCID: PMC11844735 DOI: 10.1126/sciadv.adu3011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2024] [Accepted: 01/22/2025] [Indexed: 02/23/2025]
5
Iimori Y, Morita T, Masuda T, Kitajima S, Kono N, Kageyama S, Galipon J, Sasaki AT, Kanai A. SLFN11-mediated tRNA regulation induces cell death by disrupting proteostasis in response to DNA-damaging agents. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.08.632070. [PMID: 39829761 PMCID: PMC11741311 DOI: 10.1101/2025.01.08.632070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/22/2025]
6
Muneer G, Chen C, Chen Y. Advancements in Global Phosphoproteomics Profiling: Overcoming Challenges in Sensitivity and Quantification. Proteomics 2025;25:e202400087. [PMID: 39696887 PMCID: PMC11735659 DOI: 10.1002/pmic.202400087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2024] [Revised: 11/29/2024] [Accepted: 11/29/2024] [Indexed: 12/20/2024]
7
Yamamoto T, Furukawa A, Zhou Y, Kono N, Kitajima S, Ohguchi H, Kawano Y, Ito S, Araki N, Ohtsuki S, Masuda T. Increased CSN5 expression enhances the sensitivity to lenalidomide in multiple myeloma cells. iScience 2024;27:111399. [PMID: 39687025 PMCID: PMC11647120 DOI: 10.1016/j.isci.2024.111399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 08/21/2024] [Accepted: 11/12/2024] [Indexed: 12/18/2024]  Open
8
Yamashita M, Ogawa C, Zhang B, Kobayashi T, Nomura A, Barker C, Zou C, Yamanaka S, Hayashi KI, Shinkai Y, Moro K, Fargarasan S, Imami K, Seita J, Shirai F, Sawasaki T, Kanemaki MT, Taniuchi I. Cell-type specific, inducible and acute degradation of targeted protein in mice by two degron systems. Nat Commun 2024;15:10129. [PMID: 39613744 PMCID: PMC11607430 DOI: 10.1038/s41467-024-54308-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Accepted: 11/05/2024] [Indexed: 12/01/2024]  Open
9
Torii A, Seki Y, Sasano R, Ishida Y, Nakamura K, Ito R, Iwasaki Y, Iijima K, Akiyama H. Development of a rapid and reliable method to simultaneously detect seven food allergens in processed foods using LC-MS/MS. Food Chem X 2024;23:101558. [PMID: 38984290 PMCID: PMC11231652 DOI: 10.1016/j.fochx.2024.101558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 06/06/2024] [Accepted: 06/12/2024] [Indexed: 07/11/2024]  Open
10
Yu KH, Lin WT, Chen DP. How Co-Stimulatory/Inhibitory Molecules Vary Across Immune Cell Subtypes in the Severity of Systemic Lupus Erythematosus Compared to Controls. Biomedicines 2024;12:2444. [PMID: 39595011 PMCID: PMC11591756 DOI: 10.3390/biomedicines12112444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2024] [Revised: 09/30/2024] [Accepted: 10/15/2024] [Indexed: 11/28/2024]  Open
11
Tomioka R, Ogata K, Ishihama Y. Quantitation of Host Cell Proteins by Capillary LC/IMS/MS/MS in Combination with Rapid Digestion on Immobilized Trypsin Column Under Native Conditions. Mass Spectrom (Tokyo) 2024;13:A0152. [PMID: 39296308 PMCID: PMC11409222 DOI: 10.5702/massspectrometry.a0152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Accepted: 08/25/2024] [Indexed: 09/21/2024]  Open
12
Muneer G, Chen CS, Lee TT, Chen BY, Chen YJ. A Rapid One-Pot Workflow for Sensitive Microscale Phosphoproteomics. J Proteome Res 2024;23:3294-3309. [PMID: 39038167 DOI: 10.1021/acs.jproteome.3c00862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
13
Gu K, Kumabe H, Yamamoto T, Tashiro N, Masuda T, Ito S, Ohtsuki S. Improving Proteomic Identification Using Narrow Isolation Windows with Zeno SWATH Data-Independent Acquisition. J Proteome Res 2024;23:3484-3495. [PMID: 38978496 DOI: 10.1021/acs.jproteome.4c00149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
14
Sato Y, Habara M, Hanaki S, Sharif J, Tomiyasu H, Miki Y, Shimada M. Calcineurin/NFATc1 pathway represses cellular cytotoxicity by modulating histone H3 expression. Sci Rep 2024;14:14732. [PMID: 38926604 PMCID: PMC11208570 DOI: 10.1038/s41598-024-65769-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 06/24/2024] [Indexed: 06/28/2024]  Open
15
Nishino T, Mukai H, Moriyama M, Hosokawa T, Tanahashi M, Tachikawa S, Nikoh N, Koga R, Fukatsu T. Defensive fungal symbiosis on insect hindlegs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.25.586038. [PMID: 38585921 PMCID: PMC10996522 DOI: 10.1101/2024.03.25.586038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
16
Shan B, Barker CS, Theraulaz H, Zhang X, Ping Y, Gupta RK, Shao M, Wu Y. Protocol for quantitative proteomic analysis of heterogeneous adipose tissue-residing progenitor subpopulations in mice. STAR Protoc 2023;4:102676. [PMID: 38048219 PMCID: PMC10730372 DOI: 10.1016/j.xpro.2023.102676] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/15/2023] [Accepted: 10/06/2023] [Indexed: 12/06/2023]  Open
17
Hasegawa N, Hongo M, Okada M, Kuga T, Abe Y, Adachi J, Tomonaga T, Yamaguchi N, Nakayama Y. Phosphotyrosine proteomics in cells synchronized at monopolar cytokinesis reveals EphA2 as functioning in cytokinesis. Exp Cell Res 2023;432:113783. [PMID: 37726045 DOI: 10.1016/j.yexcr.2023.113783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 09/11/2023] [Accepted: 09/12/2023] [Indexed: 09/21/2023]
18
Liu YK, Wu X, Hadisurya M, Li L, Kaimakliotis H, Iliuk A, Tao WA. One-Pot Analytical Pipeline for Efficient and Sensitive Proteomic Analysis of Extracellular Vesicles. J Proteome Res 2023;22:3301-3310. [PMID: 37702715 PMCID: PMC10897859 DOI: 10.1021/acs.jproteome.3c00361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
19
Miwa T, Taguchi H. Escherichia coli small heat shock protein IbpA plays a role in regulating the heat shock response by controlling the translation of σ32. Proc Natl Acad Sci U S A 2023;120:e2304841120. [PMID: 37523569 PMCID: PMC10410725 DOI: 10.1073/pnas.2304841120] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 06/23/2023] [Indexed: 08/02/2023]  Open
20
Dick JM, Meng D. Community- and genome-based evidence for a shaping influence of redox potential on bacterial protein evolution. mSystems 2023;8:e0001423. [PMID: 37289197 PMCID: PMC10308962 DOI: 10.1128/msystems.00014-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 02/28/2023] [Indexed: 06/09/2023]  Open
21
Hadisurya M, Lee ZC, Luo Z, Zhang G, Ding Y, Zhang H, Iliuk AB, Pili R, Boris RS, Tao WA. Data-Independent Acquisition Phosphoproteomics of Urinary Extracellular Vesicles Enables Renal Cell Carcinoma Grade Differentiation. Mol Cell Proteomics 2023;22:100536. [PMID: 36997065 PMCID: PMC10165457 DOI: 10.1016/j.mcpro.2023.100536] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 03/01/2023] [Accepted: 03/24/2023] [Indexed: 03/31/2023]  Open
22
Devlin T, Marx DC, Roskopf MA, Bubb QR, Plummer AM, Fleming KG. FkpA enhances membrane protein folding using an extensive interaction surface. Protein Sci 2023;32:e4592. [PMID: 36775935 PMCID: PMC10031210 DOI: 10.1002/pro.4592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 01/17/2023] [Accepted: 02/07/2023] [Indexed: 02/14/2023]
23
Komori Y, Niinae T, Imami K, Yanagibayashi J, Yasunaga K, Imamura S, Tomita M, Ishihama Y. Bioinertization of nanoLC/MS/MS systems by depleting metal ions from the mobile phases for phosphoproteomics. Mol Cell Proteomics 2023;22:100535. [PMID: 36958626 PMCID: PMC10172917 DOI: 10.1016/j.mcpro.2023.100535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 02/16/2023] [Accepted: 03/19/2023] [Indexed: 03/25/2023]  Open
24
Imami K, Selbach M, Ishihama Y. Monitoring mitochondrial translation by pulse SILAC. J Biol Chem 2023;299:102865. [PMID: 36603763 PMCID: PMC9922817 DOI: 10.1016/j.jbc.2022.102865] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 12/27/2022] [Accepted: 12/27/2022] [Indexed: 01/04/2023]  Open
25
Onodera H, Niwa T, Taguchi H, Chadani Y. Prophage excision switches the primary ribosome rescue pathway and rescue-associated gene regulations in Escherichia coli. Mol Microbiol 2023;119:44-58. [PMID: 36471624 PMCID: PMC10107115 DOI: 10.1111/mmi.15003] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 11/07/2022] [Accepted: 11/15/2022] [Indexed: 11/23/2022]
26
SETD1A regulates transcriptional pause release of heme biosynthesis genes in leukemia. Cell Rep 2022;41:111727. [PMID: 36450243 PMCID: PMC9771694 DOI: 10.1016/j.celrep.2022.111727] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 08/08/2022] [Accepted: 11/03/2022] [Indexed: 12/02/2022]  Open
27
Takano J, Ito S, Dong Y, Sharif J, Nakajima-Takagi Y, Umeyama T, Han YW, Isono K, Kondo T, Iizuka Y, Miyai T, Koseki Y, Ikegaya M, Sakihara M, Nakayama M, Ohara O, Hasegawa Y, Hashimoto K, Arner E, Klose RJ, Iwama A, Koseki H, Ikawa T. PCGF1-PRC1 links chromatin repression with DNA replication during hematopoietic cell lineage commitment. Nat Commun 2022;13:7159. [PMID: 36443290 PMCID: PMC9705430 DOI: 10.1038/s41467-022-34856-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 11/09/2022] [Indexed: 11/29/2022]  Open
28
Kanemaru A, Shinriki S, Kai M, Tsurekawa K, Ozeki K, Uchino S, Suenaga N, Yonemaru K, Miyake S, Masuda T, Kariya R, Okada S, Takeshita H, Seki Y, Yano H, Komohara Y, Yoshida R, Nakayama H, Li JD, Saito H, Jono H. Potential use of EGFR-targeted molecular therapies for tumor suppressor CYLD-negative and poor prognosis oral squamous cell carcinoma with chemoresistance. Cancer Cell Int 2022;22:358. [PMID: 36376983 PMCID: PMC9664721 DOI: 10.1186/s12935-022-02781-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 11/04/2022] [Indexed: 11/16/2022]  Open
29
Papadopoulos A, Busch M, Reiners J, Hachani E, Baeumers M, Berger J, Schmitt L, Jaeger KE, Kovacic F, Smits SHJ, Kedrov A. The periplasmic chaperone Skp prevents misfolding of the secretory lipase A from Pseudomonas aeruginosa. Front Mol Biosci 2022;9:1026724. [DOI: 10.3389/fmolb.2022.1026724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 09/26/2022] [Indexed: 11/13/2022]  Open
30
Mori A, Masuda T, Ito S, Ohtsuki S. Human Hepatic Transporter Signature Peptides for Quantitative Targeted Absolute Proteomics: Selection, Digestion Efficiency, and Peptide Stability. Pharm Res 2022;39:2965-2978. [PMID: 36131112 DOI: 10.1007/s11095-022-03387-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/29/2022] [Indexed: 11/28/2022]
31
Nishino K, Yoshikawa H, Motani K, Kosako H. Optimized Workflow for Enrichment and Identification of Biotinylated Peptides Using Tamavidin 2-REV for BioID and Cell Surface Proteomics. J Proteome Res 2022;21:2094-2103. [PMID: 35979633 DOI: 10.1021/acs.jproteome.2c00130] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
32
Coral holobiont cues prime Endozoicomonas for a symbiotic lifestyle. THE ISME JOURNAL 2022;16:1883-1895. [PMID: 35444262 PMCID: PMC9296628 DOI: 10.1038/s41396-022-01226-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 02/23/2022] [Accepted: 03/14/2022] [Indexed: 12/11/2022]
33
Masuda T, Inamori Y, Furukawa A, Yamahiro M, Momosaki K, Chang CH, Kobayashi D, Ohguchi H, Kawano Y, Ito S, Araki N, Ong SE, Ohtsuki S. Water Droplet-in-Oil Digestion Method for Single-Cell Proteomics. Anal Chem 2022;94:10329-10336. [PMID: 35817413 PMCID: PMC9330287 DOI: 10.1021/acs.analchem.1c05487] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
34
Zhang X, Takeuchi T, Takeda A, Mochizuki H, Nagai Y. Comparison of serum and plasma as a source of blood extracellular vesicles: Increased levels of platelet-derived particles in serum extracellular vesicle fractions alter content profiles from plasma extracellular vesicle fractions. PLoS One 2022;17:e0270634. [PMID: 35749554 PMCID: PMC9231772 DOI: 10.1371/journal.pone.0270634] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 06/15/2022] [Indexed: 11/30/2022]  Open
35
Shan B, Barker CS, Shao M, Zhang Q, Gupta RK, Wu Y. Multilayered omics reveal sex- and depot-dependent adipose progenitor cell heterogeneity. Cell Metab 2022;34:783-799.e7. [PMID: 35447091 PMCID: PMC9986218 DOI: 10.1016/j.cmet.2022.03.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 01/17/2022] [Accepted: 03/28/2022] [Indexed: 01/25/2023]
36
Ogata S, Masuda T, Ito S, Ohtsuki S. Targeted proteomics for cancer biomarker verification and validation. Cancer Biomark 2022;33:427-436. [DOI: 10.3233/cbm-210218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
37
Chaperones Skp and SurA dynamically expand unfolded OmpX and synergistically disassemble oligomeric aggregates. Proc Natl Acad Sci U S A 2022;119:2118919119. [PMID: 35217619 PMCID: PMC8892499 DOI: 10.1073/pnas.2118919119] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2022] [Indexed: 11/18/2022]  Open
38
Nagano H, Ogata S, Ito S, Masuda T, Ohtsuki S. Knockdown of podocalyxin post-transcriptionally induces the expression and activity of ABCB1/MDR1 in human brain microvascular endothelial cells. J Pharm Sci 2022;111:1812-1819. [PMID: 35182544 DOI: 10.1016/j.xphs.2022.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/11/2022] [Accepted: 02/12/2022] [Indexed: 10/19/2022]
39
Purification and Phosphoproteomic Analysis of Plasma-Derived Extracellular Vesicles. Methods Mol Biol 2022;2504:147-156. [PMID: 35467285 PMCID: PMC9437911 DOI: 10.1007/978-1-0716-2341-1_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
40
Advances in sample preparation for membrane proteome quantification. DRUG DISCOVERY TODAY. TECHNOLOGIES 2021;39:23-29. [PMID: 34906323 DOI: 10.1016/j.ddtec.2021.06.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 05/25/2021] [Accepted: 06/11/2021] [Indexed: 12/21/2022]
41
Keulers TG, Libregts SF, Beaumont JE, Savelkouls KG, Bussink J, Duimel H, Dubois L, Zonneveld MI, López‐Iglesias C, Bezstarosti K, Demmers JA, Vooijs M, Wauben M, Rouschop KM. Secretion of pro-angiogenic extracellular vesicles during hypoxia is dependent on the autophagy-related protein GABARAPL1. J Extracell Vesicles 2021;10:e12166. [PMID: 34859607 PMCID: PMC8640512 DOI: 10.1002/jev2.12166] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 10/21/2021] [Accepted: 11/02/2021] [Indexed: 12/29/2022]  Open
42
Nagano H, Ito S, Masuda T, Ohtsuki S. Effect of Insulin Receptor-Knockdown on the Expression Levels of Blood-Brain Barrier Functional Proteins in Human Brain Microvascular Endothelial Cells. Pharm Res 2021;39:1561-1574. [PMID: 34811625 DOI: 10.1007/s11095-021-03131-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 10/20/2021] [Indexed: 02/07/2023]
43
Chida K, Sakurai Y, Ohtani A, Masuda T, Ohtsuki S, Tanaka H, Akita H. Proteomics Analysis of Lymphatic Metastasis-Related Proteins Using Highly Metastatic Human Melanoma Cells Originated by Sequential in Vivo Implantation. Biol Pharm Bull 2021;44:1551-1556. [PMID: 34602565 DOI: 10.1248/bpb.b21-00463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
44
Bhandari BK, Lim CS, Remus DM, Chen A, van Dolleweerd C, Gardner PP. Analysis of 11,430 recombinant protein production experiments reveals that protein yield is tunable by synonymous codon changes of translation initiation sites. PLoS Comput Biol 2021;17:e1009461. [PMID: 34610008 PMCID: PMC8519471 DOI: 10.1371/journal.pcbi.1009461] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 10/15/2021] [Accepted: 09/19/2021] [Indexed: 12/16/2022]  Open
45
A protocol for analyzing the protein terminome of human cancer cell line culture supernatants. STAR Protoc 2021;2:100682. [PMID: 34377995 PMCID: PMC8327658 DOI: 10.1016/j.xpro.2021.100682] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]  Open
46
Shimada T, Nakazawa K, Tachikawa T, Saito N, Niwa T, Taguchi H, Tanaka K. Acetate overflow metabolism regulates a major metabolic shift after glucose depletion in Escherichia coli. FEBS Lett 2021;595:2047-2056. [PMID: 34125966 DOI: 10.1002/1873-3468.14151] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/01/2021] [Accepted: 06/07/2021] [Indexed: 11/09/2022]
47
Tsumagari K, Ishihama Y. Acylated peptide enrichment utilizing lysine deacylases for lysine acylomics. Biochem Biophys Res Commun 2021;563:60-65. [PMID: 34062387 DOI: 10.1016/j.bbrc.2021.05.077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 05/19/2021] [Indexed: 01/22/2023]
48
Suzuki T, Terada N, Higashiyama S, Kametani K, Shirai Y, Honda M, Kai T, Li W, Tabuchi K. Non-microtubule tubulin-based backbone and subordinate components of postsynaptic density lattices. Life Sci Alliance 2021;4:4/7/e202000945. [PMID: 34006534 PMCID: PMC8326785 DOI: 10.26508/lsa.202000945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 04/19/2021] [Accepted: 04/26/2021] [Indexed: 12/28/2022]  Open
49
Yokoyama T, Niinae T, Tsumagari K, Imami K, Ishihama Y, Hizukuri Y, Akiyama Y. The Escherichia coli S2P intramembrane protease RseP regulates ferric citrate uptake by cleaving the sigma factor regulator FecR. J Biol Chem 2021;296:100673. [PMID: 33865858 PMCID: PMC8144685 DOI: 10.1016/j.jbc.2021.100673] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 04/08/2021] [Accepted: 04/14/2021] [Indexed: 02/03/2023]  Open
50
Hatakeyama D, Masuda T, Miki R, Ohtsuki S, Kuzuhara T. In-vitro acetylation of SARS-CoV and SARS-CoV-2 nucleocapsid proteins by human PCAF and GCN5. Biochem Biophys Res Commun 2021;557:273-279. [PMID: 33894414 PMCID: PMC8030717 DOI: 10.1016/j.bbrc.2021.03.173] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 03/31/2021] [Indexed: 12/20/2022]
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